Counting gaps per sequence¶

We have several different ways of counting sequence gaps, and of visualising the results. By default, the count_gaps_per_seq() method returns a matrix of counts without the ability to visualise the results. When setting the argument unique=True, the counts are for gaps uniquely induced by each sequence. This can be a useful indicator of highly divergent sequences.

from cogent3 import load_aligned_seqs

aln = load_aligned_seqs('../../data/brca1.fasta', moltype='dna')

counts = aln.count_gaps_per_seq(unique=True)
counts

FlyingFox	DogFaced	FreeTaile	LittleBro	TombBat	RoundEare	FalseVamp
0	0	0	0	0	0	0

FlyingFox	LeafNose	Horse	Rhino	Pangolin	Cat	Dog	Llama	Pig	Cow	Hippo
0	0	0	0	0	0	0	0	0	3	0

FlyingFox	SpermWhale	HumpbackW	Mole	Hedgehog	TreeShrew	FlyingLem	Galago
0	0	0	0	0	3	0	3

FlyingFox	HowlerMon	Rhesus	Orangutan	Gorilla	Human	Chimpanzee	Jackrabbit
0	21	0	0	0	0	0	0

FlyingFox	FlyingSqu	OldWorld	Mouse	Rat	NineBande	HairyArma	Anteater
0	57	0	0	0	0	0	0

FlyingFox	Sloth	Dugong	Manatee	AfricanEl	AsianElep	RockHyrax	TreeHyrax
0	0	0	0	0	0	0	0

FlyingFox	Aardvark	GoldenMol	Madagascar	Tenrec	LesserEle	GiantElep
0	0	0	0	6	0	6

FlyingFox	Caenolest	Phascogale	Wombat	Bandicoot
0	0	0	0	0

Plotting counts of unique gaps¶

There are three plot types supported. In all cases, placing the mouse pointer over a data point will show hover text with the sequence name.

Displaying unique gaps as a bar chart¶

counts = aln.count_gaps_per_seq(unique=True, drawable='bar')
counts.show(width=500)

Displaying unique gaps as a violin plot¶

counts = aln.count_gaps_per_seq(unique=True, drawable='violin')
counts.show(width=300, height=500)

Displaying unique gaps as a box plot¶

counts = aln.count_gaps_per_seq(unique=True, drawable='box')
counts.show(width=300, height=500)

Total running time of the script: ( 0 minutes 0.599 seconds)

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